SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R1_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.6
Cutadapt version: 3.1
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2 --threads 28
Output file will be GZIP compressed


This is cutadapt 3.1 with Python 3.8.5
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1083.91 s (29 µs/read; 2.04 M reads/minute).

=== Summary ===

Total reads processed:              36,871,756
Reads with adapters:                16,142,874 (43.8%)
Reads written (passing filters):    36,871,756 (100.0%)

Total basepairs processed: 3,913,478,219 bp
Quality-trimmed:               6,690,699 bp (0.2%)
Total written (filtered):  3,888,601,182 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16142874 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 45.2%
  C: 10.5%
  G: 6.6%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	14740280	9217939.0	0	14740280
2	917217	2304484.8	0	917217
3	335971	576121.2	0	335971
4	146884	144030.3	0	146884
5	1359	36007.6	0	1359
6	420	9001.9	0	420
7	134	2250.5	0	134
8	35	562.6	0	35
9	199	140.7	0	16 183
10	299	35.2	1	4 295
11	64	8.8	1	1 63
12	10	2.2	1	0 10
13	1	0.5	1	0 1
24	1	0.5	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R1_val_1.fq.gz
=============================================
36871756 sequences processed in total